Merge pull request #604 from Neurosim-lab/development: PR from develo…

…pment to master - VERSION 1.0.0

PR from development to master - VERSION 1.0.0

.github/workflows/tests.yml

@@ -0,0 +1,34 @@
+name: Run NetPyNE tests
+on: [push]
+jobs:
+  Run-Tests:
+    runs-on: ubuntu-18.04
+
+    strategy:
+      matrix:
+        python-version: [3.7]
+
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v2
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Update apt-get
+        run: sudo apt-get update
+
+      - name: Install packages
+        run: sudo apt-get install python-tk python3-tables
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install -e .
+
+      - name: Test with pytest
+        run: |
+          source tests/test.sh

.gitignore

@@ -19,6 +19,7 @@ i386
 *.dll
 umac
 .DS_Store
+venv/
 
 /examples/HybridTut/*.nml
 /examples/HybridTut/*.mod
@@ -50,4 +51,4 @@ umac
 /examples/M1/*.png
 /examples/M1/*.pov
 /examples/HHTut/temp.json
-.vscode
+.vscode

CHANGES.md

@@ -1,3 +1,34 @@
+# Version 1.0.0
+
+**New features**
+
+- Added wrapper for distributed saving; can now simply replace 'sim.gatherData()' with 'sim.gatherDataFromNodes()'
+
+- Added distributed saving/loading ability (save/load data by MPI node)
+
+- Allowed to specify 'cellModel' and point neuron params in netParams.cellParams (not only in netParams.popParams) 
+
+- Added cellsVisualizationSpacingMultiplier property to netParams
+
+- Improved Granger plot, renamed it plotGranger
+
+- Added interactive Granger plot (iplotGranger)
+
+- Implemented testing in GitHub Actions with pytest (thanks Daniel!)
+
+- Improved sim.clearAll such that it works even before a sim is run
+
+- Properly formatted all module docstrings
+
+**Bug fixes**
+
+- Fixed bug in TupleToStr function
+
+- Fixed broken links in tutorials
+
+- Bokeh update required changing options from None to 'auto'
+
+
 # Version 0.9.9.1
 
 **Bug fixes**

doc/source/code/tut5.py

@@ -70,10 +70,10 @@
 
 
 simConfig.analysis['plotRaster'] = {'orderBy': 'y', 'orderInverse': True, 'saveFig': True}         # Plot a raster
-simConfig.analysis['plotTraces'] = {'include': [('E2',0), ('E4', 0), ('E5', 5)], 'saveFig': True}  # Plot recorded traces for this list of cells
-simConfig.analysis['plot2Dnet'] = {'saveFig': True}                                                # plot 2D cell positions and connections
-simConfig.analysis['plotConn'] = {'saveFig': True}                                                 # plot connectivity matrix
-
+# simConfig.analysis['plotTraces'] = {'include': [('E2',0), ('E4', 0), ('E5', 5)], 'saveFig': True}  # Plot recorded traces for this list of cells
+# simConfig.analysis['plot2Dnet'] = {'saveFig': True}                                                # plot 2D cell positions and connections
+# simConfig.analysis['plotConn'] = {'saveFig': True}                                                 # plot connectivity matrix
+#simConfig.analysis['plot2Dfiring'] = {'saveFig': True, 'showFig': True}
 
 # Create network and run simulation
 sim.createSimulateAnalyze(netParams = netParams, simConfig = simConfig)

doc/source/code/tut7.py

@@ -16,7 +16,7 @@
 netParams.cellParams['PYR'] = {'secs': secs}  # add dict to list of cell properties
 
 # Population parameters
-netParams.popParams['hop'] = {'cellType': 'PYR', 'cellModel': 'HH', 'numCells': 50}     # add dict with params for this pop
+netParams.popParams['hop'] = {'cellType': 'PYR', 'numCells': 50}     # add dict with params for this pop
 #netParams.popParams['background'] = {'cellModel': 'NetStim', 'rate': 50, 'noise': 0.5}  # background inputs
 
 # Synaptic mechanism parameters

doc/source/code/tut8_batch.py

@@ -8,7 +8,6 @@ def batchTauWeight():
         # fill in with parameters to explore and range of values (key has to coincide with a variable in simConfig)
         params['synMechTau2'] = [3.0, 5.0, 7.0]
         params['connWeight'] = [0.005, 0.01, 0.15]
-        params[('analysis', 'plotTraces', 'saveFig')] = [True, False]
 
         # create Batch object with parameters to modify, and specifying files to use
         b = Batch(params=params, cfgFile='tut8_cfg.py', netParamsFile='tut8_netParams.py',)

doc/source/code/tut_artif.py

@@ -16,13 +16,26 @@
 ###############################################################################
 
 # Population parameters
-netParams.popParams['PYR1'] = {'cellModel': 'HH', 'cellType': 'PYR', 'numCells': 100} # pop of HH cells
-netParams.popParams['artif1'] = {'cellModel': 'NetStim', 'numCells': 100, 'rate': 50, 'noise': 0.8, 'start': 1, 'seed': 2}  # pop of NetStims
-netParams.popParams['artif2'] = {'cellModel': 'IntFire2', 'numCells': 100, 'ib': 0.0}  # pop of IntFire2
-netParams.popParams['artif3'] = {'cellModel': 'IntFire4', 'numCells': 100, 'taue': 1.0}  # pop of IntFire4
-netParams.popParams['artif4'] = {'cellModel': 'VecStim', 'numCells': 100, 'rate': 5, 'noise': 0.5, 'start': 50,
+netParams.popParams['PYR1'] = {'cellType': 'PYR', 'numCells': 100} # pop of HH cells
+netParams.popParams['artif1'] = {'cellType': 'artif_NetStim', 'numCells': 100}  # pop of NetStims
+netParams.popParams['artif2'] = {'cellType': 'artif_IntFire2', 'numCells': 100}  # pop of IntFire2
+netParams.popParams['artif3'] = {'cellType': 'artif_IntFire4', 'numCells': 100}  # pop of IntFire4
+netParams.popParams['artif4'] = {'cellType': 'artif_VecStim', 'numCells': 100}  # pop of Vecstims with 2 pulses
+
+# Cell parameters
+## PYR cell properties
+cellParams = Dict()
+cellParams.secs.soma.geom = {'diam': 18.8, 'L': 18.8, 'Ra': 123.0}
+cellParams.secs.soma.mechs.hh = {'gnabar': 0.12, 'gkbar': 0.036, 'gl': 0.003, 'el': -70}
+netParams.cellParams['PYR'] = cellParams
+
+netParams.cellParams['artif_NetStim'] = {'cellModel': 'NetStim', 'rate': 50, 'noise': 0.8, 'start': 1, 'seed': 2}  # pop of NetStims
+netParams.cellParams['artif_IntFire2'] = {'cellModel': 'IntFire2', 'ib': 0.0}  # pop of IntFire2
+netParams.cellParams['artif3_IntFire4'] = {'cellModel': 'IntFire4', 'taue': 1.0}  # pop of IntFire4
+netParams.cellParams['artif4_Vecstim'] = {'cellModel': 'VecStim', 'rate': 5, 'noise': 0.5, 'start': 50,
     'pulses': [{'start': 200, 'end': 300, 'rate': 60, 'noise':0.2}, {'start': 500, 'end': 800, 'rate': 30, 'noise': 0.5}]}  # pop of Vecstims with 2 pulses
 
+
 # Synaptic mechanism parameters
 netParams.synMechParams['AMPA'] = {'mod': 'Exp2Syn', 'tau1': 0.1, 'tau2': 1.0, 'e': 0}
 
@@ -32,31 +45,25 @@
 netParams.stimTargetParams['bkg->PYR1'] = {'source': 'background', 'conds': {'pop': 'PYR1'}, 'sec':'soma', 'loc': 0.5, 'weight': 0.5, 'delay': 1}
 
 
-# Cell parameters
-## PYR cell properties
-cellParams = Dict()
-cellParams.secs.soma.geom = {'diam': 18.8, 'L': 18.8, 'Ra': 123.0}
-cellParams.secs.soma.mechs.hh = {'gnabar': 0.12, 'gkbar': 0.036, 'gl': 0.003, 'el': -70}
-cellParams.conds = {'cellType': 'PYR'}
-netParams.cellParams['PYR'] = cellParams
-
-
 # Connections
 netParams.connParams['artif1->PYR1'] = {
-    'preConds': {'pop': 'artif1'}, 'postConds': {'pop': 'PYR1'},
+    'preConds': {'pop': 'artif1'}, 
+    'postConds': {'pop': 'PYR1'},
     'convergence': 8,
     'weight': 0.005,
     'synMech': 'AMPA',
     'delay': 'uniform(1,5)'}
 
 netParams.connParams['PYR1->artif2'] = {
-    'preConds': {'pop': 'PYR1'}, 'postConds': {'pop': 'artif2'},
+    'preConds': {'pop': 'PYR1'}, 
+    'postConds': {'pop': 'artif2'},
     'probability': 0.2,
     'weight': 0.2,
     'delay': 'uniform(1,5)'}
 
 netParams.addConnParams('artif2->artif3',
-    {'preConds': {'pop': 'artif2'}, 'postConds': {'pop': 'artif3'},
+    {'preConds': {'pop': 'artif2'}, 
+    'postConds': {'pop': 'artif3'},
     'divergence': 20,
     'weight': 0.05,
 	'delay': 3})

doc/source/conf.py

@@ -60,9 +60,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.9.9.1'
+version = '1.0.0'
 # The full version, including alpha/beta/rc tags.
-release = '0.9.9.1'
+release = '1.0.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/source/tutorial.rst

@@ -924,7 +924,7 @@ The first example ( :download:`cell_lfp.py <../../examples/LFPrecording/cell_lfp
 	:width: 60%
 	:align: center
 
-The second example ( :download:`net_lfp.py <<../../examples/LFPrecording/net_lfp.py>`) shows LFP recording for a network very similar to that shown in Tutorial 5. However, in this case, the cells have been replaced with a more realistic model: a 6-compartment M1 corticostriatal neuron with multiple ionic channels. The cell parameters are loaded from a .json file. Cell receive NetStim inputs and include excitatory and inhibitory connections. Four LFP electrodes are placed at different cortical depths. The raster plot and LFP time-resolved signal, PSD, spectrogram and 3D locations of the electrodes are plotted:
+The second example ( :download:`net_lfp.py <../../examples/LFPrecording/net_lfp.py>`) shows LFP recording for a network very similar to that shown in Tutorial 5. However, in this case, the cells have been replaced with a more realistic model: a 6-compartment M1 corticostriatal neuron with multiple ionic channels. The cell parameters are loaded from a .json file. Cell receive NetStim inputs and include excitatory and inhibitory connections. Four LFP electrodes are placed at different cortical depths. The raster plot and LFP time-resolved signal, PSD, spectrogram and 3D locations of the electrodes are plotted:
 
 .. image:: figs/lfp_net.png
 	:width: 90%
@@ -937,7 +937,7 @@ Tutorial 10: Network with Reaction-Diffusion (RxD)
 NetPyNE's high-level specifications also supports `NEURON's reaction-diffusion (RxD) <https://www.neuron.yale.edu/neuron/static/docs/rxd/index.html>`_  components. RxD enables to specify the diffusion of molecules (\eg\ calcium, potassium or IP3) intracellularly, subcellularly (by including organelles such as endoplasmic reticulum and mitochondria), and extracellularly is the context of signaling and enzymatic processing -- \eg\ metabolism, phosphorylation, buffering, second messenger cascades.
 This helps to couple molecular-level chemophysiology to the classical electrophysiology at subcellular, cellular and network scales. 
 
-The ``netParams.rxdParams`` dictionary can be used to define the different RxD components: ``regions``, ``species``, ``states``, ``reactions``, ``multicompartmentReactions`` and ``rates``. Example models that include RxD components in single cells and networks are included in the \examples folder: `RxD buffering example <https://github.com/Neurosim-lab/netpyne/tree/development/examples/rxd_buffering>`_ and `RxD network example <https://github.com/Neurosim-lab/netpyne/tree/development/examples/rxd_network>`_. RxD also works with parallel simulations.
+The ``netParams.rxdParams`` dictionary can be used to define the different RxD components: ``regions``, ``species``, ``states``, ``reactions``, ``multicompartmentReactions`` and ``rates``. Example models that include RxD components in single cells and networks are included in the \examples folder: `RxD buffering example <https://github.com/Neurosim-lab/netpyne/tree/development/examples/rxd_buffering>`_ and `RxD network example <https://github.com/Neurosim-lab/netpyne/tree/development/examples/rxd_net>`_. RxD also works with parallel simulations.
 
 
 

examples/HybridTut/HybridTut.py

@@ -22,13 +22,13 @@
 ###############################################################################
 
 # Population parameters
-netParams.popParams['PYR_HH'] = {'cellModel': 'HH', 'cellType': 'PYR', 'numCells': 50} # add dict with params for this pop
-netParams.popParams['PYR_Izhi'] = {'cellModel': 'Izhi', 'cellType': 'PYR', 'numCells': 50} # add dict with params for this pop
+netParams.popParams['PYR_HH_pop'] = {'cellType': 'PYR_HH', 'numCells': 50} # add dict with params for this pop
+netParams.popParams['PYR_Izhi_pop'] = {'cellType': 'PYR_Izhi', 'numCells': 50} # add dict with params for this pop
 
 
 # Cell parameters list
 ## PYR cell properties (HH)
-cellRule = {'conds': {'cellType': 'PYR', 'cellModel': 'HH'},  'secs': {}}
+cellRule = {'secs': {}}
 cellRule['secs']['soma'] = {'geom': {}, 'topol': {}, 'mechs': {}}  # soma properties
 cellRule['secs']['soma']['geom'] = {'diam': 6.3, 'L': 5, 'Ra': 123.0, 'pt3d':[]}
 cellRule['secs']['soma']['geom']['pt3d'].append((0, 0, 0, 20))
@@ -43,7 +43,7 @@
 netParams.cellParams['PYR_HH'] = cellRule  # add dict to list of cell properties
 
 ## PYR cell properties (Izhi)
-cellRule = {'conds': {'cellType': 'PYR', 'cellModel': 'Izhi'},  'secs': {}}
+cellRule = {'secs': {}}
 cellRule['secs']['soma'] = {'geom': {}, 'pointps':{}}  # soma properties
 cellRule['secs']['soma']['geom'] = {'diam': 10, 'L': 10, 'cm': 31.831}
 cellRule['secs']['soma']['pointps']['Izhi'] = {'mod':'Izhi2007b',
@@ -57,15 +57,16 @@
 
 # Stimulation parameters
 netParams.stimSourceParams['bkg'] = {'type': 'NetStim', 'rate': 10, 'noise': 0.5}
-netParams.stimTargetParams['bg->PYR_Izhi'] = {'source': 'bkg', 'conds': {'cellType': 'PYR', 'cellModel': 'Izhi'},
+netParams.stimTargetParams['bg->PYR_Izhi'] = {'source': 'bkg', 'conds': {'cellType': 'PYR_Izhi'},
                                             'weight': 1, 'delay': 'uniform(1,5)', 'synMech': 'AMPA'}
-netParams.stimTargetParams['bg->PYR_HH'] = {'source': 'bkg', 'conds': {'cellType': 'PYR', 'cellModel': 'HH'},
+netParams.stimTargetParams['bg->PYR_HH'] = {'source': 'bkg', 'conds': {'cellType': 'PYR_HH'},
                                             'weight': 1, 'synMech': 'AMPA', 'sec': 'dend', 'loc': 1.0, 'delay': 'uniform(1,5)'}
 
 
 # Connectivity parameters
 netParams.connParams['PYR->PYR'] = {
-    'preConds': {'cellType': 'PYR'}, 'postConds': {'cellType': 'PYR'},
+    'preConds': {'cellType': ['PYR_HH', 'PYR_Izhi']}, 
+    'postConds': {'cellType': ['PYR_HH', 'PYR_Izhi']},
     'weight': 0.2,                    # weight of each connection
     'delay': '0.2+normal(13.0,1.4)',     # delay min=0.2, mean=13.0, var = 1.4
     'threshold': 10,                    # threshold
@@ -112,4 +113,3 @@
 # Analysis and plotting
 simConfig.analysis['plotRaster'] = {'orderInverse': False} #True # Whether or not to plot a raster
 simConfig.analysis['plotTraces'] = {'include': [1,51]} # plot recorded traces for this list of cells
-simConfig.analysis['plotRatePSD'] = {'include': ['allCells', 'PYR_HH', 'PYR_Izhi'], 'smooth': 10} # plot recorded traces for this list of cells

examples/LFPrecording/cell_lfp.py

@@ -35,8 +35,8 @@
 
 simConfig.analysis['plotTraces'] = {'include': [('E',0)], 'oneFigPer':'cell', 'overlay': True, 'figSize': (5,3),'saveFig': True}      # Plot recorded traces for this list of cells
 simConfig.analysis['plotLFP'] = {'includeAxon': False, 'plots': ['timeSeries',  'locations'], 'figSize': (5,9), 'saveFig': True}
-simConfig.analysis['getCSD'] = {'timeRange': [10,45],'spacing_um': 150, 'vaknin': True}
-simConfig.analysis['plotCSD'] = {'LFP_overlay':True}
+#simConfig.analysis['getCSD'] = {'timeRange': [10,45],'spacing_um': 150, 'vaknin': True}
+simConfig.analysis['plotCSD'] = {'timeRange': [10,45]}
 #sim.analysis.getCSD(...args...)
 #simConfig.analysis['plotCSD'] = {}
 

examples/LFPrecording/net_lfp.py

@@ -47,7 +47,7 @@
 
 # Simulation configuration
 simConfig = specs.SimConfig()        # object of class SimConfig to store simulation configuration
-simConfig.duration = 3.0*1e3           # Duration of the simulation, in ms
+simConfig.duration = 300 #3.0*1e3           # Duration of the simulation, in ms
 simConfig.dt = 0.1                # Internal integration timestep to use
 simConfig.verbose = False            # Show detailed messages
 simConfig.recordStep = 1             # Step size in ms to save data (eg. V traces, LFP, etc)
@@ -59,7 +59,7 @@
 simConfig.analysis['plotLFP'] = {'includeAxon': False, 'figSize': (6,10), 'timeRange': [100,3000], 'saveFig': True} 
 #simConfig.analysis['getCSD'] = {'spacing_um': 200, 'timeRange': [100,3000], 'vaknin': True}
 #simConfig.analysis['plotLFP'] = {'includeAxon': False, 'figSize': (6,10), 'timeRange':[100,900], 'minFreq': 10, 'maxFreq':60, 'norm':1, 'plots': ['spectrogram'], 'showFig': True} 
-simConfig.analysis['plotCSD'] = {'timeRange':[100,3000]}
+simConfig.analysis['plotCSD'] = {'timeRange':[100,200]}
 
 # Create network and run simulation
 sim.createSimulateAnalyze(netParams = netParams, simConfig = simConfig)    

netpyne/__init__.py

@@ -4,7 +4,7 @@
 NetPyNE consists of a number of sub-packages and modules.
 """
 
-__version__ = '0.9.9.1'
+__version__ = '1.0.0'
 import os, sys
 display = os.getenv('DISPLAY')
 nogui = (sys.argv.count('-nogui')>0)

netpyne/analysis/__init__.py

@@ -22,13 +22,14 @@
 # Import utils methods
 # -------------------------------------------------------------------------------------------------------------------
 from .utils import exception, _showFigure, _saveFigData, getCellsInclude, getCellsIncludeTags, _roundFigures, \
-     _smooth1d, syncMeasure, invertDictMapping
+     _smooth1d, syncMeasure, invertDictMapping, checkAvailablePlots
 
 
 # -------------------------------------------------------------------------------------------------------------------
 # Import connectivity-related functions
 # -------------------------------------------------------------------------------------------------------------------
-from .network import plotConn, _plotConnCalculateFromSim, _plotConnCalculateFromFile, plot2Dnet, plotShape, calculateDisynaptic
+from .network import plotConn, _plotConnCalculateFromSim, _plotConnCalculateFromFile, plot2Dnet, plotShape, calculateDisynaptic, \
+    plot2Dfiring
 
 
 # -------------------------------------------------------------------------------------------------------------------
@@ -53,7 +54,7 @@
 # -------------------------------------------------------------------------------------------------------------------
 # Import information theory-related functions
 # -------------------------------------------------------------------------------------------------------------------
-from .info import nTE, granger
+from .info import nTE, granger, plotGranger
 
 
 # -------------------------------------------------------------------------------------------------------------------
@@ -67,7 +68,7 @@
 # -------------------------------------------------------------------------------------------------------------------
 
 try:
-  from .interactive import iplotDipole, iplotDipoleSpectrogram, iplotDipolePSD, iplotRaster, iplotSpikeHist, iplotRatePSD, iplotTraces, iplotLFP, iplotConn, iplotRxDConcentration, iplot2Dnet, iplotSpikeStats
+  from .interactive import iplotDipole, iplotDipoleSpectrogram, iplotDipolePSD, iplotRaster, iplotSpikeHist, iplotRatePSD, iplotTraces, iplotLFP, iplotConn, iplotRxDConcentration, iplot2Dnet, iplotSpikeStats, iplotGranger
 except:
     print('Warning: could not import interactive plotting functions; make sure the "bokeh" package is installed.')